One of the issues I've ran into with the simulator is you need a pretty fast computer to run it properly. I have a somewhat fast computer with lots of memory. I have CH yoke and it runs OK with that, but generally I just run it with the autopilot because it's pretty much worthless otherwise.
On slower computers I've notices many of the modules periodically lock up and I notice the red-x on several of the functions, which may be what you're experiencing although the autopilot may not have a red-x to denote when it momentarily goes inop.
If you buy the deluxe version of MS Flight Sim X, it has a few G1000 aircraft, including the 172. There's a few functions missing as compared to the Garmin simulator, but it isn't bad.
I used MS flight Sim X, the Garmin simulator, and Max Trescott's book to train with. By the time I got into the real thing I still had lots to learn, but I was definitely way ahead of the game.